Align FAA hydrolase family protein (characterized, see rationale)
to candidate 353409 BT3883 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase (NCBI ptt file)
Query= uniprot:A0A2E7P912 (281 letters) >FitnessBrowser__Btheta:353409 Length = 204 Score = 102 bits (253), Expect = 9e-27 Identities = 67/181 (37%), Positives = 96/181 (53%), Gaps = 5/181 (2%) Query: 72 KFICIGLNYADHAAE-SNLPIPAEPVVFNKWTSAVVGPNDDVKIPRGSKKTDWEVELGVV 130 K I +G+NYA H E + + EPV+F K SA++ IP S + +E EL V Sbjct: 2 KIIAVGMNYALHNQELGHTSVNKEPVIFMKPDSAILKDGKPFFIPDFSNEVHYETELVVR 61 Query: 131 IGKGGSYIDEKDAMSHVAGYCVVNDVSEREYQI---ERGGTWDKGKGCDTFGPIGPWLVT 187 I + G I + A + V D + R+ Q E G W+ KG D+ IG + V Sbjct: 62 INRLGKNISPRFASRYYDALTVGIDFTARDLQRKFREAGNPWELCKGFDSSAAIGTF-VP 120 Query: 188 RDEVADPQKLGMWLEVDGKRYQNGNTSTMIFGVAHIVSYLSRFMSLQPGDVISTGTPPGV 247 D D Q L L +DGK Q G T+ M+F V I++Y+S+F++L+ GD++ TGTP GV Sbjct: 121 VDRYKDIQSLNFNLMIDGKEVQRGCTADMLFKVDDIIAYVSKFVTLKIGDLLFTGTPAGV 180 Query: 248 G 248 G Sbjct: 181 G 181 Lambda K H 0.316 0.138 0.419 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 155 Number of extensions: 9 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 281 Length of database: 204 Length adjustment: 23 Effective length of query: 258 Effective length of database: 181 Effective search space: 46698 Effective search space used: 46698 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 bits) S2: 46 (22.3 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory